Post List

  • June 16, 2010
  • 08:48 AM
  • 490 views

Snake in the grass

by admin in U+003F

One aim of this blog was to advocate and advertise the use of open science. Which is somewhat at odds with my advocation and advertisement of Matlab – a popular, powerful, but ultimately pricey piece of software. I’ve spent some time working with Octave – a language that is identical in every way to Matlab, [...]... Read more »

Michael Barnsley, John E. Hutchinson, & Örjan Stenflo. (2003) V-variable fractals and superfractals. -. arXiv: math/0312314v1

  • June 16, 2010
  • 08:47 AM
  • 494 views

Paper of the Week : A Whale of the waste matter

by Sarah Stephen in An ecological oratorio

The way by which living organisms in our planet are intricately connected is beautiful beyond comprehension. Like pieces in a puzzle they all fit together with the activities of each organism however trivial it may appear to be, affecting the existance of others. We will never fully understand this marvel, but a noteworthy example is the elegant finding by Lavery et al published in the Proceedings of the Royal Society (Biological Sciences)- Iron defecation by sperm whales stimulates carbon expo........ Read more »

Lavery, T., Roudnew, B., Gill, P., Seymour, J., Seuront, L., Johnson, G., Mitchell, J., & Smetacek, V. (2010) Iron defecation by sperm whales stimulates carbon export in the Southern Ocean. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2010.0863  

  • June 16, 2010
  • 08:45 AM
  • 442 views

Tip of the Week: Biocatalogue for finding web services

by Mary in OpenHelix


A couple of years back at a conference I was introduced to Biocatalogue.  It seemed to me to be a really useful idea: locate bioinformatics tools and databases that are web-accessible, and that also have a mechanism to use the web service features to access the tool/server using strategies that don’t require the main web interface of the site.  There are some introductions  to the concept of web services out there–some of them are more for introduction, but most are aimed at prog........ Read more »

Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., Wolstencroft, K., Aleksejevs, S., Stevens, R., Pettifer, S.... (2010) BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research. DOI: 10.1093/nar/gkq394  

  • June 16, 2010
  • 08:30 AM
  • 699 views

Sugar preference: beyond the tongue

by Colby in nutsci.org






In studies, rodents generally prefer sugars over amino acids/proteins when given the choice, and this seems to reflect their ability to bind to the sweet T1R2/T1R3 receptor on the tongue.  Postingestion, however, nutrients obviously differentially effect hormones involved in fuel mobilization (e.g. insulin and glucagon), so mechanisms should exist to influence appetite for specific macronutrients. [...]... Read more »

Ren, X., Ferreira, J., Zhou, L., Shammah-Lagnado, S., Yeckel, C., & de Araujo, I. (2010) Nutrient Selection in the Absence of Taste Receptor Signaling. Journal of Neuroscience, 30(23), 8012-8023. DOI: 10.1523/JNEUROSCI.5749-09.2010  

  • June 16, 2010
  • 08:01 AM
  • 1,472 views

The impact of vessel traffic on riverine fish

by Rob Goldstein in Conservation Maven

... Read more »

  • June 16, 2010
  • 08:00 AM
  • 2,051 views

Obesity Compounds Pain in Fibromyalgia

by Arya M. Sharma in Dr. Sharma's Obesity Notes

As blogged before, overweight and obese patients frequently present with fibromyalgia, characterized by chronic pain, fatigue and depressed mood.
A paper by Akiko Okifuji from the University of Utah, Salt Lake City, just published in the Journal of Pain, examines the relationship between fibromyalgia and obesity in pain, function, mood, and sleep.
The study examines the impact [...]... Read more »

Okifuji A, Donaldson GW, Barck L, & Fine PG. (2010) Relationship Between Fibromyalgia and Obesity in Pain, Function, Mood, and Sleep. The journal of pain : official journal of the American Pain Society. PMID: 20542742  

  • June 16, 2010
  • 07:45 AM
  • 1,212 views

How Specific Are The Social Skills of Dogs?

by Jason Goldman in The Thoughtful Animal

Dogs are particularly good at tasks that involve communicating or cooperating with humans, which has led some researchers to speculate that they are really good at solving social tasks, more generally. For example, dogs can figure out where a human's attention is, are really good at picking up on eye-gaze and finger pointing cues, distinguish among different individual humans (by contrast, humans are really bad at distinguishing among different individual monkeys, for example), and at least in o........ Read more »

  • June 16, 2010
  • 06:00 AM
  • 661 views

Escape velocity

by David Winter in Careers - in Theory

A recent survey of over 4,000 UK employees conducted by GfK NOP found that one in four were planning to leave their organisation within the next year. The survey suggests these intentions are linked to the actions taken by the employers dealing with the effects of the recession. Continuing measures such as redundancies, recruitment freezes, [...]... Read more »

Brockner, J. (1992) Managing the effects of layoffs on survivors. California Management Review, 34(2), 9-28. info:/

Appelbaum, S., Delage, C., Labib, N., & Gault, G. (1997) The survivor syndrome: aftermath of downsizing. Career Development International, 2(6), 278-286. DOI: 10.1108/13620439710178639  

  • June 16, 2010
  • 05:29 AM
  • 1,194 views

Tourette's Syndrome associated with superior timing control

by BPS Research Digest in BPS Research Digest

Children with Tourette's Syndrome, the neurodevelopmental condition characterised by involuntary motor and verbal tics, have superior timing abilities compared with their healthy age-matched peers, a new study suggests.Carmelo Vicario and colleagues tested nine children with Tourette's (average age 11 years) and 10 controls (average age 12) on timing perception and timing production. The former involved the children judging whether two circles were on screen for the same length of time or not. T........ Read more »

Vicario, C., Martino, D., Spata, F., Defazio, G., Giacchè, R., Martino, V., Rappo, G., Pepi, A., Silvestri, P., & Cardona, F. (2010) Time processing in children with Tourette’s syndrome. Brain and Cognition, 73(1), 28-34. DOI: 10.1016/j.bandc.2010.01.008  

  • June 16, 2010
  • 04:51 AM
  • 706 views

Tuatara holds clues to human evolution

by hilaryml in Chicken or Egg blog

A while ago I wrote about the value of genome sequences, not just for helping us understand the biology of a particular organism, but also for enabling large-scale comparisons across species that can help spot patterns in genome evolution which wouldn’t otherwise be apparent.  A recent paper in Journal of Heredity by Craig Lowe, David Haussler and [...]... Read more »

Lowe, C., Bejerano, G., Salama, S., & Haussler, D. (2010) Endangered Species Hold Clues to Human Evolution. Journal of Heredity. DOI: 10.1093/jhered/esq016  

  • June 16, 2010
  • 03:48 AM
  • 1,196 views

time-on-task effects in fMRI research: why you should care

by Tal Yarkoni in citation needed

There’s a ubiquitous problem in experimental psychology studies that use behavioral measures that require participants to make speeded responses. The problem is that, in general, the longer people take to do something, the more likely they are to do it correctly. If I have you do a visual search task and ask you to tell [...]... Read more »

  • June 16, 2010
  • 01:27 AM
  • 867 views

What does that MRI signal MEAN, anyway?

by Evil Monkey in Neurotopia

Sci was incredibly excited to see this paper come out. It's got lots of stuff going for it, and all its powers combined were enough to send Sci bouncing around in her seat and sending emails to Ed Yong saying "OMG COOL PAPER!!".

What's it got, you say? It's got the meaning of life, the universe, and that pesky MRI signal.

Lee et al. "Global and local fMRI signals driven by neurons defined optogenetically by type and wiring" Nature, 2010.



Ah, the pretty brain picture. But what does it........ Read more »

Lee, J., Durand, R., Gradinaru, V., Zhang, F., Goshen, I., Kim, D., Fenno, L., Ramakrishnan, C., & Deisseroth, K. (2010) Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Nature, 465(7299), 788-792. DOI: 10.1038/nature09108  

  • June 16, 2010
  • 12:42 AM
  • 382 views

…Results – Just hook it up to my veins

by Rift in Psycasm

Last week I wrote about the potential impacts of caffeine (in coffee and energy drinks) on students and their study (here). In short, however, these were what I considered the most relevant findings: Keleman and Creeley (2001)found that Caffeine reliably improves hit rates for sustained attention, that there was an interaction between caffeine and free [...]... Read more »

  • June 15, 2010
  • 11:47 PM
  • 1,622 views

Reflections on the Gulf Oil Spill - Conversations With My Grandpa

by Christie Wilcox in Observations of a Nerd

Yes, it would be great if we never spilled a drop of oil. No matter how hard we may try, though, the fact is that nobody is perfect, and oil spills are an inevitable consequence of our widespread use of oil. The question is, once the oil is out there, how do we clean it up? Perhaps my grandfather put it best, when I asked him what he thought about how BP and the US is responding to the spill.

"They're friggin' idiots."... Read more »

Jonathan L. Ramseur. (2010) Oil Spills in U.S. Coastal Waters: Background, Governance, and Issues for Congress. Congressional Research Service , 7-5700 (RL33705). info:/

Paine, R., Ruesink, J., Sun, A., Soulanille, E., Wonham, M., Harley, C., Brumbaugh, D., & Secord, D. (1996) TROUBLE ON OILED WATERS: Lessons from the Exxon Valdez Oil Spill. Annual Review of Ecology and Systematics, 27(1), 197-235. DOI: 10.1146/annurev.ecolsys.27.1.197  

  • June 15, 2010
  • 11:18 PM
  • 1,233 views

Why Oil-Laden Prey is Bad for Sea Birds

by Kevin Zelnio in Deep Sea News


Oil is bad for wildlife. Period. But we really do not understand how it is bad. What does it do? Can marine organisms respond physiologically to oil in diets? For instance, translocate the toxic components to feathers and molt it off, much like some crabs, or have other physiologically mechanisms to . . . → Read More: Why Oil-Laden Prey is Bad for Sea Birds... Read more »

  • June 15, 2010
  • 10:45 PM
  • 948 views

Biodiversity SNAFU in Australia’s Jewel

by CJA Bradshaw in ConservationBytes

I’ve covered this sad state of affairs and one of Australia’s more notable biodiversity embarrassments over the last year (see Shocking continued loss of Australian mammals and Can we solve Australia’s mammal extinction crisis?), and now the most empirical demonstration of this is now published. The biodiversity guru of Australia’s tropical north, John Woinarksi, has [...]... Read more »

Woinarski, J., Armstrong, M., Brennan, K., Fisher, A., Griffiths, A., Hill, B., Milne, D., Palmer, C., Ward, S., Watson, M.... (2010) Monitoring indicates rapid and severe decline of native small mammals in Kakadu National Park, northern Australia. Wildlife Research, 37(2), 116. DOI: 10.1071/WR09125  

  • June 15, 2010
  • 08:27 PM
  • 1,289 views

Repost: Mosasaurs - The Marine Monsters of New Jersey

by Laelaps in Laelaps



The skull of Mosasaurus hoffmani. From Lingham-Soliar 1995.


On my first trip to the Inversand marl pit in Sewell, New Jersey, I didn't find the wonderfully preserved Dryptosaurus skeleton I had been dreaming of. I picked up a number of Cretaceous bivalve shells and Paleocene sponges, but other than a few scraps of "Chunkosaurus" my excavations didn't yield very much. Before my paleontology class left the site, though, we took a walk by the spoil piles - great green mounds of sediment that ha........ Read more »

  • June 15, 2010
  • 07:46 PM
  • 2,267 views

Facilitated Communication: A Review of the Literature (with a new introduction)

by KWombles in Countering...

Three months ago, I ran the post that appears below. This post got lots of comments, and there were a fair number of misunderstandings, so let me up-front here make clear what I mean by facilitated communication in the hopes these misunderstandings do not occur again. We teach our children many skills by using hand-over-hand techniques. I'm not talking about teaching your child how to type, how to hold a pencil, how to do things. I'm talking specifically about the facilitated communication as Bi........ Read more »

  • June 15, 2010
  • 06:50 PM
  • 2,347 views

Will Climate Change Alter Sea Turtle Populations to the Point of Extinction?

by Scott A. in Thriving Oceans

Our planet is an intriguing concoction of variables that meld together for successes spanning the organization of life (species, populations, communities, and ecosystems).  It is literally an evolutionary process that is ecologically driven.  And as a genotypic sex determined species, we seem to have an inherent fascination with the mysterious adaptive significance of environmental sex [...]... Read more »

  • June 15, 2010
  • 04:48 PM
  • 1,343 views

A little incentive goes a long way when it comes to vaccine uptake

by geekheartsscience in geek!

Offering people free lentils and metal food dishes substantially improves the number of young children that receive a full course of childhood immunisations in resource poor areas, and is more cost effective than just improving the vaccine services available in the region, according to a new study published free in the British Medical Journal. Abhijit [...]... Read more »

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